Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition

Zhang, Chenyu; Han, Rungang; Zhang, Anru R.; Voyles, Paul. M.

doi:10.1016/j.ultramic.2020.113123

Title: Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition

Journal Article · Mon Oct 05 00:00:00 EDT 2020 · Ultramicroscopy

DOI:https://doi.org/10.1016/j.ultramic.2020.113123· OSTI ID:1849893

Zhang, Chenyu ^[1]; Han, Rungang ^[2]; Zhang, Anru R. ^[2]; Voyles, Paul. M. ^[1]

Univ. of Wisconsin, Madison, WI (United States). Dept. of Materials Science and Engineering
Univ. of Wisconsin, Madison, WI (United States). Dept. of Statistics

Tensor singular value decomposition (SVD) is a method to find a low-dimensional representation of data with meaningful structure in three or more dimensions. Here, tensor SVD has been applied to denoise atomic-resolution 4D scanning transmission electron microscopy (4D STEM) data. On data simulated from a SrTiO₃ [100] perfect crystal and a Si [110] edge dislocation, tensor SVD achieved an average peak signal-to-noise ratio (PSNR) of ~40 dB, which matches or exceeds the performance of other denoising methods, with processing times at least 100 times shorter. On experimental data from SrTiO₃ [100] and LiZnSb [11 $\bar{2}$ 0]/GaSb [110] samples, tensor SVD denoises multiple GB 4D STEM data sets in ten minutes on a typical personal computer. Denoising with tensor SVD improves both convergent beam electron diffraction patterns and virtual-aperture annular dark field images.

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Research Organization:: Univ. of Wisconsin, Madison, WI (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); National Institutes of Health (NIH)

Grant/Contract Number:: FG02-08ER46547; DMS-1811868; CAREER-1944904; DMR-1720415; R01-GM131399

OSTI ID:: 1849893

Alternate ID(s):: OSTI ID: 1809538

Journal Information:: Ultramicroscopy, Vol. 219, Issue C; ISSN 0304-3991

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (48)

Multitask Sparse Nonnegative Matrix Factorization for Joint Spectral–Spatial Hyperspectral Imagery Denoising Ye, Minchao; Qian, Yuntao; Zhou, Jun IEEE Transactions on Geoscience and Remote Sensing, Vol. 53, Issue 5 https://doi.org/10.1109/TGRS.2014.2363101	journal	May 2015
Atomic resolution convergent beam electron diffraction analysis using convolutional neural networks Zhang, Chenyu; Feng, Jie; DaCosta, Luis Rangel Ultramicroscopy, Vol. 210 https://doi.org/10.1016/j.ultramic.2019.112921	journal	March 2020
Method to measure spatial coherence of subangstrom electron beams Dwyer, Christian; Erni, Rolf; Etheridge, Joanne Applied Physics Letters, Vol. 93, Issue 2 https://doi.org/10.1063/1.2957648	journal	July 2008
Quantitative characterization of nanoprecipitates in irradiated low-alloy steels: advances in the application of FEG-STEM quantitative microanalysis to real materials Burke, M. G.; Watanabe, M.; Williams, D. B. Journal of Materials Science, Vol. 41, Issue 14 https://doi.org/10.1007/s10853-006-0084-x	journal	July 2006
Tensor SVD: Statistical and Computational Limits Zhang, Anru; Xia, Dong IEEE Transactions on Information Theory, Vol. 64, Issue 11 https://doi.org/10.1109/TIT.2018.2841377	journal	November 2018
Total Variation Regularized Reweighted Sparse Nonnegative Matrix Factorization for Hyperspectral Unmixing He, Wei; Zhang, Hongyan; Zhang, Liangpei IEEE Transactions on Geoscience and Remote Sensing, Vol. 55, Issue 7 https://doi.org/10.1109/TGRS.2017.2683719	journal	July 2017
Chemical mapping of a block copolymer electrolyte by low-loss EFTEM spectrum-imaging and principal component analysis Allen, F. I.; Watanabe, M.; Lee, Z. Ultramicroscopy, Vol. 111, Issue 3 https://doi.org/10.1016/j.ultramic.2010.11.035	journal	February 2011
Hyperspectral image restoration using framelet-regularized low-rank nonnegative matrix factorization Chen, Yong; Huang, Ting-Zhu; Zhao, Xi-Le Applied Mathematical Modelling, Vol. 63 https://doi.org/10.1016/j.apm.2018.06.044	journal	November 2018
Principal component analysis Wold, Svante; Esbensen, Kim; Geladi, Paul Chemometrics and Intelligent Laboratory Systems, Vol. 2, Issue 1-3 https://doi.org/10.1016/0169-7439(87)80084-9	journal	August 1987
The global k-means clustering algorithm Likas, Aristidis; Vlassis, Nikos; J. Verbeek, Jakob Pattern Recognition, Vol. 36, Issue 2 https://doi.org/10.1016/S0031-3203(02)00060-2	journal	February 2003
Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM Li, Xueming; Mooney, Paul; Zheng, Shawn Nature Methods, Vol. 10, Issue 6 https://doi.org/10.1038/nmeth.2472	journal	May 2013
Phase reconstruction using fast binary 4D STEM data O'Leary, C. M.; Allen, C. S.; Huang, C. Applied Physics Letters, Vol. 116, Issue 12 https://doi.org/10.1063/1.5143213	journal	March 2020
Noise Reduction of Hyperspectral Images Using Kernel Non-Negative Tucker Decomposition Karami, A.; Yazdi, M.; Zolghadre Asli, Alireza IEEE Journal of Selected Topics in Signal Processing, Vol. 5, Issue 3 https://doi.org/10.1109/JSTSP.2011.2132692	journal	June 2011
Image Denoising by Sparse 3-D Transform-Domain Collaborative Filtering Dabov, Kostadin; Foi, Alessandro; Katkovnik, Vladimir IEEE Transactions on Image Processing, Vol. 16, Issue 8 https://doi.org/10.1109/TIP.2007.901238	journal	August 2007
An adaptive rank-sparsity K-SVD algorithm for image sequence denoising Kuang, Yin; Zhang, Lei; Yi, Zhang Pattern Recognition Letters, Vol. 45 https://doi.org/10.1016/j.patrec.2014.03.003	journal	August 2014
Optimal Sparse Singular Value Decomposition for High-Dimensional High-Order Data Zhang, Anru; Han, Rungang Journal of the American Statistical Association, Vol. 114, Issue 528 https://doi.org/10.1080/01621459.2018.1527227	journal	March 2019
Control of polymorphism during epitaxial growth of hyperferroelectric candidate LiZnSb on GaSb (111)B Du, Dongxue; Strohbeen, Patrick J.; Paik, Hanjong Journal of Vacuum Science & Technology B, Vol. 38, Issue 2 https://doi.org/10.1116/1.5145217	journal	March 2020
Strain mapping at nanometer resolution using advanced nano-beam electron diffraction Ozdol, V. B.; Gammer, C.; Jin, X. G. Applied Physics Letters, Vol. 106, Issue 25 https://doi.org/10.1063/1.4922994	journal	June 2015
Structure change of Ca _{1− x} Sr _x TiO ₃ perovskite with composition and pressure Yamanaka, Takamitsu; Hirai, Noriyuki; Komatsu, Yutaka American Mineralogist, Vol. 87, Issue 8-9 https://doi.org/10.2138/am-2002-8-917	journal	August 2002
High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy Tate, Mark W.; Purohit, Prafull; Chamberlain, Darol Microscopy and Microanalysis, Vol. 22, Issue 1 https://doi.org/10.1017/S1431927615015664	journal	January 2016
On the Best Rank-1 and Rank-( R ₁ , R ₂ ,. . ., R _N ) Approximation of Higher-Order Tensors De Lathauwer, Lieven; De Moor, Bart; Vandewalle, Joos SIAM Journal on Matrix Analysis and Applications, Vol. 21, Issue 4 https://doi.org/10.1137/S0895479898346995	journal	January 2000
A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy Pryor, Alan; Ophus, Colin; Miao, Jianwei Advanced Structural and Chemical Imaging, Vol. 3, Issue 1 https://doi.org/10.1186/s40679-017-0048-z	journal	October 2017
Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM): From Scanning Nanodiffraction to Ptychography and Beyond Ophus, Colin Microscopy and Microanalysis, Vol. 25, Issue 3 https://doi.org/10.1017/S1431927619000497	journal	May 2019
Atomic electric fields revealed by a quantum mechanical approach to electron picodiffraction Müller, Knut; Krause, Florian F.; Béché, Armand Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms6653	journal	December 2014
EELS elemental mapping with unconventional methods I. Theoretical basis: Image analysis with multivariate statistics and entropy concepts Trebbia, Pierre; Bonnet, Noël Ultramicroscopy, Vol. 34, Issue 3 https://doi.org/10.1016/0304-3991(90)90070-3	journal	December 1990
Denoising time-resolved microscopy image sequences with singular value thresholding Furnival, Tom; Leary, Rowan K.; Midgley, Paul A. Ultramicroscopy, Vol. 178 https://doi.org/10.1016/j.ultramic.2016.05.005	journal	July 2017
Direct observation of Σ7 domain boundary core structure in magnetic skyrmion lattice Matsumoto, Takao; So, Yeong-Gi; Kohno, Yuji Science Advances, Vol. 2, Issue 2 https://doi.org/10.1126/sciadv.1501280	journal	February 2016
Convergent beam electron diffraction of multilayer Van der Waals structures Latychevskaia, Tatiana; Woods, Colin Robert; Wang, Yi Bo Ultramicroscopy, Vol. 212 https://doi.org/10.1016/j.ultramic.2020.112976	journal	May 2020
Nonlocal Transform-Domain Filter for Volumetric Data Denoising and Reconstruction Maggioni, M.; Katkovnik, V.; Egiazarian, K. IEEE Transactions on Image Processing, Vol. 22, Issue 1 https://doi.org/10.1109/TIP.2012.2210725	journal	January 2013
Automatic denoising of functional MRI data: Combining independent component analysis and hierarchical fusion of classifiers Salimi-Khorshidi, Gholamreza; Douaud, Gwenaëlle; Beckmann, Christian F. NeuroImage, Vol. 90 https://doi.org/10.1016/j.neuroimage.2013.11.046	journal	April 2014
On the Tensor SVD and the Optimal Low Rank Orthogonal Approximation of Tensors Chen, Jie; Saad, Yousef SIAM Journal on Matrix Analysis and Applications, Vol. 30, Issue 4 https://doi.org/10.1137/070711621	journal	January 2009
Video Denoising, Deblocking, and Enhancement Through Separable 4-D Nonlocal Spatiotemporal Transforms Maggioni, Matteo; Boracchi, Giacomo; Foi, Alessandro IEEE Transactions on Image Processing, Vol. 21, Issue 9 https://doi.org/10.1109/TIP.2012.2199324	journal	September 2012
Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing, and Storage Nord, Magnus; Webster, Robert W. H.; Paton, Kirsty A. Microscopy and Microanalysis, Vol. 26, Issue 4 https://doi.org/10.1017/S1431927620001713	journal	July 2020
Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy McMullan, G.; Faruqi, A. R.; Clare, D. Ultramicroscopy, Vol. 147 https://doi.org/10.1016/j.ultramic.2014.08.002	journal	December 2014
Picometre-precision analysis of scanning transmission electron microscopy images of platinum nanocatalysts Yankovich, Andrew B.; Berkels, Benjamin; Dahmen, W. Nature Communications, Vol. 5, Issue 1 https://doi.org/10.1038/ncomms5155	journal	June 2014
MULTIVARIATE STATISTICAL ANALYSIS OF FEG-STEM EDX SPECTRA Titchmarsh, J. M.; Dumbill, S. Journal of Microscopy, Vol. 184, Issue 3 https://doi.org/10.1046/j.1365-2818.1996.1400698.x	journal	December 1996
Mapping chemical and bonding information using multivariate analysis of electron energy-loss spectrum images Bosman, M.; Watanabe, M.; Alexander, D. T. L. Ultramicroscopy, Vol. 106, Issue 11-12, p. 1024-1032 https://doi.org/10.1016/j.ultramic.2006.04.016	journal	October 2006
Observation of three-dimensional elemental distributions of a Si device using a 360°-tilt FIB and the cold field-emission STEM system Yaguchi, Toshie; Konno, Mitsuru; Kamino, Takeo Ultramicroscopy, Vol. 108, Issue 12, p. 1603-1615 https://doi.org/10.1016/j.ultramic.2008.06.003	journal	November 2008
Non-rigid registration and non-local principle component analysis to improve electron microscopy spectrum images Yankovich, Andrew B.; Zhang, Chenyu; Oh, Albert Nanotechnology, Vol. 27, Issue 36 https://doi.org/10.1088/0957-4484/27/36/364001	journal	August 2016
On the Origin of Nanochessboard Superlattices in A-Site-Deficient Ca-Stabilized Nd _2/3 TiO ₃ Azough, Feridoon; Kepaptsoglou, Demie; Ramasse, Quentin M. Chemistry of Materials, Vol. 27, Issue 2 https://doi.org/10.1021/cm5036985	journal	January 2015
Poisson noise removal from high-resolution STEM images based on periodic block matching Mevenkamp, Niklas; Binev, Peter; Dahmen, Wolfgang Advanced Structural and Chemical Imaging, Vol. 1, Issue 1 https://doi.org/10.1186/s40679-015-0004-8	journal	March 2015
Measurement of effective source distribution and its importance for quantitative interpretation of STEM images Dwyer, C.; Erni, R.; Etheridge, J. Ultramicroscopy, Vol. 110, Issue 8 https://doi.org/10.1016/j.ultramic.2010.01.007	journal	July 2010
Independent component analysis: algorithms and applications Hyvärinen, A.; Oja, E. Neural Networks, Vol. 13, Issue 4-5 https://doi.org/10.1016/S0893-6080(00)00026-5	journal	June 2000
Fluctuation microscopy in the STEM Voyles, P. M.; Muller, D. A. Ultramicroscopy, Vol. 93, Issue 2 https://doi.org/10.1016/S0304-3991(02)00155-9	journal	November 2002
Informatics and data science in materials microscopy Voyles, Paul M. Current Opinion in Solid State and Materials Science, Vol. 21, Issue 3 https://doi.org/10.1016/j.cossms.2016.10.001	journal	June 2017
Algorithms and applications for approximate nonnegative matrix factorization Berry, Michael W.; Browne, Murray; Langville, Amy N. Computational Statistics & Data Analysis, Vol. 52, Issue 1 https://doi.org/10.1016/j.csda.2006.11.006	journal	September 2007
Sub-100 nanosecond temporally resolved imaging with the Medipix3 direct electron detector Paterson, Gary W.; Lamb, Raymond J.; Ballabriga, Rafael Ultramicroscopy, Vol. 210 https://doi.org/10.1016/j.ultramic.2019.112917	journal	March 2020
Direct determination of structural heterogeneity in metallic glasses using four-dimensional scanning transmission electron microscopy Im, Soohyun; Chen, Zhen; Johnson, Jared M. Ultramicroscopy, Vol. 195 https://doi.org/10.1016/j.ultramic.2018.09.005	journal	December 2018

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Title: Denoising atomic resolution 4D scanning transmission electron microscopy data with tensor singular value decomposition

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